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You certainly don't have to add an agent via the dT client. On the application server you can add the agent mapping details directly into the JVM options of a java based application such as a Tomcat application or launch the .net configuration editor and add a .net app that way.

As far as "automating" it through a command line, some java applications like a Tomcat application probably have their JVM options stored in the registry which you could manipulate via the command line. It doesn't look like the .net configuration editor has any additonal parameters associated with the dtagentconf.exe. Perhaps it would be a good feature enhancement?

For .NET you could do the following
a) configure one machine using the .NET Agent configuration Tool
b) export the registry entries that the .NET Config Tool writes -> look at HKLM\Software\Wow6432Node\dynaTrace\Agent\WhiteList
c) import these registry keys on your other .NET Servers